Better error message for unsorted BAM

[jakobnissen]

Dear @apcamargo

Thanks for the heads-up on this package. It looks great! I'm giving it a test spin now. When passing a non-sorted BAM:

>>> pycoverm.get_coverages_from_bam(["out.bam"], threads=4)
thread '<unnamed>' panicked at 'called `Result::unwrap()` on an `Err` value: ShapeError/IncompatibleShape: incompatible shapes', src/lib.rs:181:6
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
pyo3_runtime.PanicException: called `Result::unwrap()` on an `Err` value: ShapeError/IncompatibleShape: incompatible shapes

A better error-message would be preferrable (I would perhaps do a search-and-replace for unwrap() and replace it with expect("<NEW ERROR MESSAGE>"))

[apcamargo]

Yes, I still need to implement a function to check if BAMs are sorted. I'll make it raise an exception.

The reason I haven't implemented this yet is because I'm doing this check in Python (see below), but I agree with you that pyCoverM should be able to do it within itself to avoid unnecessary dependencies.

from Bio import bgzf

def is_bam_sorted(filepath):
    """
    Checks if a BAM file is sorted by coordinate.
    Parameters
    ----------
    filepath : Path
        Path object pointing to BAM file.
    Returns
    -------
    bool
        Returns `True` if the BAM file is sorted by coordinate and `False`
        otherwise.
    """
    with bgzf.BgzfReader(filepath, "rb") as fin:
        bam_header = fin.readline().strip()
        return b"SO:coordinate" in bam_header

[apcamargo]

I just pushed some commits that add the is_bam_sorted, which can be used to check if the BAMs are sorted before inputting them to get_coverages_from_bam.

To check multiple files:

if not all(pycoverm.is_bam_sorted(bam_path) for bam_path in bam_file_list):
    raise Exception(
        "At least one of the supplied BAM files is not sorted by coordinate "
        "or does not contain a valid header. You can sort it using `samtools sort`."
    )

I'll leave the issue open because this function doesn't fix it properly. When I get some time I'll make get_coverages_from_bam raise an exception if at least one of the input BAM files is unsorted.